scholarly journals Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

2018 ◽  
pp. 225-240 ◽  
Author(s):  
Zhemin Zhou ◽  
Nina Luhmann ◽  
Nabil-Fareed Alikhan ◽  
Christopher Quince ◽  
Mark Achtman
Keyword(s):  
Metagenomic Sequencing ◽  
Microbial Strains ◽  
Reference Genomes ◽  
Accurate Reconstruction

scholarly journals Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

2017 ◽  
Author(s):  
Zhemin Zhou ◽  
Nina Luhmann ◽  
Nabil-Fareed Alikhan ◽  
Christopher Quince ◽  
Mark Achtman
Keyword(s):  
Evaluation Studies ◽  
Species Level ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Reference Databases ◽  
Microbial Strains ◽  
Taxonomic Assignments ◽  
Taxonomic Groups ◽  
Reference Genomes ◽  
Recent Evaluation

AbstractExploring the genetic diversity of microbes within the environment through metagenomic sequencing first requires classifying these reads into taxonomic groups. Current methods compare these sequencing data with existing biased and limited reference databases. Several recent evaluation studies demonstrate that current methods either lack sufficient sensitivity for species-level assignments or suffer from false positives, overestimating the number of species in the metagenome. Both are especially problematic for the identification of low-abundance microbial species, e. g. detecting pathogens in ancient metagenomic samples. We present a new method, SPARSE, which improves taxonomic assignments of metagenomic reads. SPARSE balances existing biased reference databases by grouping reference genomes into similarity-based hierarchical clusters, implemented as an efficient incremental data structure. SPARSE assigns reads to these clusters using a probabilistic model, which specifically penalizes non-specific mappings of reads from unknown sources and hence reduces false-positive assignments. Our evaluation on simulated datasets from two recent evaluation studies demonstrated the improved precision of SPARSE in comparison to other methods for species-level classification. In a third simulation, our method successfully differentiated multiple co-existing Escherichia coli strains from the same sample. In real archaeological datasets, SPARSE identified ancient pathogens with ≤ 0.02% abundance, consistent with published findings that required additional sequencing data. In these datasets, other methods either missed targeted pathogens or reported non-existent ones. SPARSE and all evaluation scripts are available at https://github.com/zheminzhou/SPARSE.

scholarly journals Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

2018 ◽  
Author(s):  
Erik L. Clarke ◽  
Louis J. Taylor ◽  
Chunyu Zhao ◽  
Andrew Connell ◽  
Jung-Jin Lee ◽  
...  
Keyword(s):  
Cluster Computing ◽  
Workflow Management ◽  
Software Tool ◽  
Direct Analysis ◽  
Low Complexity ◽  
Single Step ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Reference Genomes ◽  
Adapter Trimming

AbstractBackgroundAnalysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes.ResultsWe present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. Unique components of the Sunbeam pipeline include direct analysis of data from NCBI SRA and an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated.ConclusionsSunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic low complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.

scholarly journals Profiling microbial strains in urban environments using metagenomic sequencing data

2018 ◽  
Vol 13 (1) ◽  
Author(s):  
Moreno Zolfo ◽  
Francesco Asnicar ◽  
Paolo Manghi ◽  
Edoardo Pasolli ◽  
Adrian Tett ◽  
...  
Keyword(s):  
Urban Environments ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Microbial Strains

PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data

2020 ◽  
Author(s):  
Shuai Wang ◽  
Yiqi Jiang ◽  
Shuaicheng Li
Keyword(s):  
Optimization Method ◽  
Supplementary Information ◽  
Marker Genes ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing ◽  
Genotype Frequencies ◽  
Microbial Strains ◽  
And Control ◽  
First Time

Abstract Motivation The microbial community plays an essential role in human diseases and physiological activities. The functions of microbes can differ due to strain-level differences in the genome sequences. Shotgun metagenomic sequencing allows us to profile the strains in microbial communities practically. However, current methods are underdeveloped due to the highly similar sequences among strains. We observe that strains genotypes at the same single nucleotide variant (SNV) locus can be speculated by the genotype frequencies. Also, the variants in different loci covered by the same reads can provide evidence that they reside on the same strain. Results These insights inspire us to design PStrain, an optimization method that utilizes genotype frequencies and the reads which cover multiple SNV loci to profile strains iteratively based on SNVs in a set of MetaPhlAn2 marker genes. Compared to the state-of-art methods, PStrain, on average, improved the performance of inferring strains abundances and genotypes by 87.75% and 59.45%, respectively. We have applied the PStrain package to the dataset with two cohorts of colorectal cancer (CRC) and found that the sequences of Bacteroides coprocola strains are significantly different between CRC and control samples, which is the first time to report the potential role of B.coprocola in the gut microbiota of CRC. Availabilityand implementation https://github.com/wshuai294/PStrain. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Individualized recovery of gut microbial strains post antibiotics

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Hyunmin Koo ◽  
Joseph A. Hakim ◽  
David K. Crossman ◽  
Ranjit Kumar ◽  
Elliot J. Lefkowitz ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Metagenomic Sequencing ◽  
Human Gastrointestinal Tract ◽  
Genomic Variants ◽  
Transient Strain ◽  
Recovery Pattern ◽  
Microbial Strains ◽  
Microbial Genomic ◽  
The Impact

Abstract To further understand the impact of antibiotics on the gastrointestinal tract microbial community, the intra-individual recovery pattern of specific microbial strains was determined using metagenomic sequencing coupled with strain-tracking analyses. In a study where 18 individuals were administered a single antibiotic (cefprozil), new microbial genomic variants (herein strains) were transiently detected in 15 individuals, while in a second study that used a cocktail of three antibiotics (meropenem, gentamicin, and vancomycin), all 12 participants had either permanent or transient strain changes. The presence of distinct microbial genomic variants indicates a pattern of strain recovery that is intra-individual specific following disruption of the human gastrointestinal tract with antibiotics.

Carum copticum L. essential oils as natural antimicrobial and antioxidant

2018 ◽  
Vol 44 (4) ◽  
pp. 515-520
Author(s):  
M Kazemi
Keyword(s):  
Essential Oils ◽  
Radical Scavenging Activity ◽  
Radical Scavenging ◽  
Dpph Radical ◽  
Dpph Radical Scavenging Activity ◽  
Carum Copticum ◽  
Microbial Strains ◽  
Pharmaceutical Industries ◽  
Dpph Radical Scavenging ◽  
Antioxidant Effects

Carum copticum L. comprises several relevant species for food, cosmetic, perfumery and pharmaceutical industries. GC/MS analysis of the enential oil of C. copticum revealed γ- terpinene as a major component of C. copticum, with its contribution of 33.85%. Essential oils (EOs) exhibited a significant antimicrobial activity against all tested microbial strains. In addition, the C. copticum oil demonstrated the highest DPPH radical scavenging activity. These results clearly show the antimicrobial and antioxidant effects of the plant essential oil.

Preliminary in Vitro Investigations on The Inhibitory Activity of The Original Dietary Supplement Oxidal® on Pathogenic Bacterial Strains

2020 ◽  
Vol 11 ◽  
pp. 37-43
Author(s):  
Prof. Teodora P. Popova ◽  
Toshka Petrova ◽  
Ignat Ignatov ◽  
Stoil Karadzhov
Keyword(s):  
Dietary Supplement ◽  
Broad Spectrum ◽  
Pathogenic Bacteria ◽  
Antimicrobial Agents ◽  
Clinical Effectiveness ◽  
Inhibitory Effect ◽  
Diffusion Method ◽  
Bacterial Strains ◽  
Microbial Strains

The antimicrobial action of the dietary supplement Oxidal® was tested using the classic Bauer and Kirby agar-gel diffusion method. Clinical and reference strains of Staphylococcus aureus and Escherichia coli were used in the studies. The tested dietary supplement showed a well-pronounced inhibitory effect against the microbial strains commensurable with that of the broad-spectrum chemotherapeutic agent Enrofloxacin and showed even higher activity than the broad spectrum antibiotic Thiamphenicol. The proven inhibitory effect of the tested dietary supplement against the examined pathogenic bacteria is in accordance with the established clinical effectiveness standards for antimicrobial agents.

The In vitro Evaluation of the Antimicrobial Activity of Quercus robur L. Methanolic and Aqueous Leaves’ Extracts, from the Algerian High Plateaus Against some Uropathogenic Microbial Strains

2019 ◽  
Vol 18 (5) ◽  
pp. 262-274
Author(s):  
E. Benyagoub ◽  
N. Nabbou ◽  
S. Boukhalkhel ◽  
I. Dehini
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Antimicrobial Activity ◽  
Candida Albicans ◽  
Enterococcus Faecalis ◽  
Fusidic Acid ◽  
Quercus Robur ◽  
Diffusion Method ◽  
Phytochemical Analysis ◽  
Microbial Strains

The medicinal value of the plants is due to their chemical components that bring a definite physiological action on the human body to prevent the diseases. In this work, we investigated the antimicrobial activity of leaves’ extracts of Quercus robur L., collected from the Algerian upper highlands, on ten bacterial strains and one fungal strain known to be pathogenic. First, we performed a qualitative phytochemical analysis, and second, antimicrobial activity tests performed by agar diffusion method (disc and well) with the determination of MIC by broth macro-dilution method. Given the results, it appears that obtained macerates of Quercus robur L. were rich in bioactive phytoconstituents such as alkaloids, anthraquinones, saponins, tannins, and other components. The yield of aqueous and methanolic macerates of leaves was 8.5 ± 1.41 and 22.4 ± 4.36%, respectively. The bacterial resistance was relatively important to several antibiotics, namely, ampicillin, amoxicillin + clavulanic acid for strains of Escherichia coli and Salmonella sp. However, Staphylococcus aureus strains were resistant to fusidic acid, penicillin, and oxacillin; while Enterococcus faecalis was resistant to fusidic acid, penicillin, oxacillin, and ticarcillin. The antibacterial activity of the macerates toward tested microbial strains showed that the aqueous and methanolic macerates of the leaves were proportional to the tested concentration and active not only against Gram-positive and Gram-negative bacteria but also on the fungal species Candida albicans. The estimated MIC for Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus was in the order of 10 mg/mL, which seems more effective than toward Salmonella sp., Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans which were in the order of 30 mg/mL. These preliminary results confirm that the part of the studied plant had a very good antimicrobial activity that was proportional to the serial concentrations of the tested extracts.

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